Re: [galaxy-dev] Towards Galaxy Linux (not) ? [was [RFC] Storing of tarballs and patches for tool_dependencies to enable reproducibility]

2013-09-20 Thread Björn Grüning
Hi Ido, > If I might chime in, I am a bit worried about all the automatic installation > going on in galaxy, and it seems that the trend is to enhance this. > A small R or python script calling into well known libraries that come from > well known repositories (bioconductor etc… ) I can check. >

Re: [galaxy-dev] Towards Galaxy Linux (not) ? [was [RFC] Storing of tarballs and patches for tool_dependencies to enable reproducibility]

2013-09-19 Thread Ido Tamir
If I might chime in, I am a bit worried about all the automatic installation going on in galaxy, and it seems that the trend is to enhance this. A small R or python script calling into well known libraries that come from well known repositories (bioconductor etc… ) I can check. (Of course I insta

Re: [galaxy-dev] Towards Galaxy Linux (not) ? [was [RFC] Storing of tarballs and patches for tool_dependencies to enable reproducibility]

2013-09-19 Thread Bjoern Gruening
Hi Simon, thank you very much for your comments! > I can see man years of effort being spent on solving this problem within > Galaxy. I was going to title this email "Danger, Will Robinson", but I > didn't want to be disrespectful. > I think the path being embarked upon, tool dependency pack

Re: [galaxy-dev] Towards Galaxy Linux (not) ? [was [RFC] Storing of tarballs and patches for tool_dependencies to enable reproducibility]

2013-09-18 Thread Peter Cock
On Wed, Sep 18, 2013 at 2:24 AM, Guest, Simon wrote: > Hi Bjoern, > > I can see man years of effort being spent on solving this problem within > Galaxy. I was going to title this email "Danger, Will Robinson", but I didn't > want to be disrespectful. I think the path being embarked upon, tool > d

[galaxy-dev] Towards Galaxy Linux (not) ? [was [RFC] Storing of tarballs and patches for tool_dependencies to enable reproducibility]

2013-09-17 Thread Guest, Simon
Hi Bjoern, I can see man years of effort being spent on solving this problem within Galaxy. I was going to title this email "Danger, Will Robinson", but I didn't want to be disrespectful. I think the path being embarked upon, tool dependency packaging, tool versioning, reproducibility, and lo